keyword
MENU ▼
Read by QxMD icon Read
search

BirA

keyword
https://www.readbyqxmd.com/read/29123507/utilizing-biotinylated-proteins-expressed-in-yeast-to-visualize-dna-protein-interactions-at-the-single-molecule-level
#1
Huijun Xue, Yuanyuan Bei, Zhengyan Zhan, Xiuqiang Chen, Xin Xu, Yu V Fu
Much of our knowledge in conventional biochemistry has derived from bulk assays. However, many stochastic processes and transient intermediates are hidden when averaged over the ensemble. The powerful technique of single-molecule fluorescence microscopy has made great contributions to the understanding of life processes that are inaccessible when using traditional approaches. In single-molecule studies, quantum dots (Qdots) have several unique advantages over other fluorescent probes, such as high brightness, extremely high photostability, and large Stokes shift, thus allowing long-time observation and improved signal-to-noise ratios...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29091714/first-evidence-of-ancient-deer-cervid-in-the-late-miocene-bira-formation-northern-israel
#2
Alexis Gabriel Rozenbaum, Dotan Shaked Gelband, Mordechai Stein, Henk K Mienis, Rivka Rabinovich
Despite the extensive geological and paleontological searches in the south Levant, no terrestrial fauna of late Neogene age was yet reported. Here, we report the first evidence of "ancient deer"-cervid in the late Miocene (Tortonian) lacustrine section of the Bira Formation at Hagal Stream, Jordan Valley, northern Israel. The section comprises rich assemblage of macrofauna fossils, mostly freshwater mollusks. The mammalian bone was discovered among the macrofauna fossils, and is described as an almost complete left humerus of an adult animal identified as an artiodactyls element probably of a cervid...
2017: PloS One
https://www.readbyqxmd.com/read/29046906/target-and-identify-triazene-linker-helps-identify-azidation-sites-of-labelled-proteins-via-click-and-cleave-strategy
#3
Jonas Lohse, Alexandra Schindl, Natasha Danda, Chris P Williams, Karl Kramer, Bernhard Kuster, Martin D Witte, Guillaume Médard
A method for identifying probe modification of proteins via tandem mass spectrometry was developed. Azide bearing molecules are immobilized on functionalised sepharose beads via copper catalysed Huisgen-type click chemistry and selectively released under acidic conditions by chemical cleavage of the triazene linkage. We applied this method to identify the modification site of targeted-diazotransfer on BirA.
October 19, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28982715/capturing-the-asc1p-rack1-microenvironment-at-the-head-region-of-the-40s-ribosome-with-quantitative-bioid-in-yeast
#4
Nadine Opitz, Kerstin Schmitt, Verena Hofer-Pretz, Bettina Neumann, Heike Krebber, Gerhard H Braus, Oliver Valerius
The Asc1 protein of Saccharomyces cerevisiae is a scaffold protein at the head region of ribosomal 40S that links mRNA translation to cellular signaling. In this study, proteins that co-localize with Asc1p were identified with proximity-dependent Biotin IDentification (BioID), an in vivo labeling technique described here for the first time for yeast. Biotinylated Asc1p-birA*-proximal proteins were identified and quantitatively verified against controls applying SILAC and mass spectrometry. The mRNA-binding proteins Sro9p and Gis2p appeared together with Scp160p, each providing ribosomes with nuclear transcripts...
October 5, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28956755/nuclear-transcriptomes-at-high-resolution-using-retooled-intact
#5
Mauricio Reynoso, Germain Pauluzzi, Kaisa Kajala, Sean Cabanlit, Joel Velasco, Jérémie Bazin, Roger Deal, Neelima Sinha, Siobhan M Brady, Julia Bailey-Serres
Isolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here we describe transfer of the Isolation of Nuclei from TAgged specific Cell Types (INTACT) to the monocot rice (Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer nuclear envelope-targeting domain of the Nuclear Tagging Fusion (NTF) protein with an outer nuclear envelope-anchored domain. This modified NTF was combined with codon optimized E...
September 27, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28942842/a-green-fluorescent-protein-based-assay-for-high-throughput-ligand-binding-studies-of-a-mycobacterial-biotin-protein-ligase
#6
Thomas E H Bond, Alanna E Sorenson, Patrick M Schaeffer
Biotin protein ligase (BirA) has been identified as an emerging drug target in Mycobacterium tuberculosis due to its essential metabolic role. Indeed, it is the only enzyme capable of covalently attaching biotin onto the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase. Despite recent interest in this protein, there is still a gap in cost-effective high-throughput screening assays for rapid identification of mycobacterial BirA-targeting inhibitors. We present for the first time the cloning, expression, purification of mycobacterial GFP-tagged BirA and its application for the development of a high-throughput assay building on the principle of differential scanning fluorimetry of GFP-tagged proteins...
December 2017: Microbiological Research
https://www.readbyqxmd.com/read/28860039/the-use-of-bira-bap-system-to-study-the-effect-of-us2-and-us11-on-mhc-class-i-heavy-chain-in-cells
#7
S Gauthami, Deepak Kumar, K S R SivaSai, Nagendra R Hegde
Biotinylation has been extensively used for antibody tagging, affinity-based purification, and in protein/DNA-protein interaction studies. Here we describe the use of biotinylation to study the turn-over of proteins in cells. We use the prokaryotic biotin ligase (BirA) to biotinylate the human leukocyte antigen (HLA)-A2 (A2) heavy chain (HC), which was engineered to contain a biotin acceptor peptide (BAP). Controlled availability of biotin in combination with visualization using streptavidin-conjugated peroxidase made it possible to detect biotinylated BAP-A2...
August 30, 2017: Immunology Letters
https://www.readbyqxmd.com/read/28776712/distinct-changing-profiles-of-hepatitis-a-and-e-virus-infection-among-patients-with-acute-hepatitis-in-mongolia-the-first-report-of-the-full-genome-sequence-of-a-novel-genotype-1-hepatitis-e-virus-strain
#8
Bira Tsatsralt-Od, Putu Prathiwi Primadharsini, Tsutomu Nishizawa, Hiroshi Ohnishi, Shigeo Nagashima, Masaharu Takahashi, Suljid Jirintai, Dulmaa Nyamkhuu, Hiroaki Okamoto
In January 2012, Mongolia started a hepatitis A vaccination program, which has not yet been evaluated. The first occurrence of autochthonous acute hepatitis E in 2013, caused by genotype 4 hepatitis E virus (HEV), suggests the need for a routine study to monitor its prevalence. One hundred fifty-four consecutive patients who were clinically diagnosed with acute hepatitis between 2014 and 2015 in Ulaanbaatar, Mongolia were studied. By serological and molecular testing followed by sequencing and phylogenetic analysis, only one patient (0...
August 4, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28718281/long-distance-modulation-of-disorder-to-order-transitions-in-protein-allostery
#9
Jingheng Wang, Gregory Custer, Dorothy Beckett, Silvina Matysiak
Elucidation of the molecular details of allosteric communication between distant sites in a protein is key to understanding and manipulating many biological regulatory processes. Although protein disorder is acknowledged to play an important thermodynamic role in allostery, the molecular mechanisms by which this disorder is harnessed for long distance communication are known for a limited number of systems. Transcription repression by the Escherichia coli biotin repressor, BirA, is allosterically activated by binding of the small molecule effector biotinoyl-5'-AMP...
August 29, 2017: Biochemistry
https://www.readbyqxmd.com/read/28636190/uch-l1-promotes-invasion-of-breast-cancer-cells-through-activating-akt-signaling-pathway
#10
Yanhong Luo, Jianfeng He, Chunlin Yang, Matthew Orange, Xingcong Ren, Nick Blair, Tao Tan, Jin-Ming Yang, Hua Zhu
As a de-ubiquitin enzyme, ubiquitin C-terminal hydrolase (UCH)-L1 has been shown to be overexpressed in several human cancers. However, the function of UCH-L1 in invasion of breast cancers is still unclear. Here we report that the expression of UCH-L1 is significantly higher in cancer cells with higher invasive ability. While ectopic UCH-L1 expression failed to alter cell proliferation in MCF-7 cells, it caused a significant upregulation of cellular invasion. Furthermore, siRNA mediated knockdown of UCH-L1 led to suppression of invasion in UCH-L1 overexpressing MCF-7 cells...
June 21, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28573017/a-crispr-cas9-high-throughput-genome-editing-toolkit-for-kinetoplastids
#11
Tom Beneke, Ross Madden, Laura Makin, Jessica Valli, Jack Sunter, Eva Gluenz
Clustered regularly interspaced short palindromic repeats (CRISPR), CRISPR-associated gene 9 (Cas9) genome editing is set to revolutionize genetic manipulation of pathogens, including kinetoplastids. CRISPR technology provides the opportunity to develop scalable methods for high-throughput production of mutant phenotypes. Here, we report development of a CRISPR-Cas9 toolkit that allows rapid tagging and gene knockout in diverse kinetoplastid species without requiring the user to perform any DNA cloning. We developed a new protocol for single-guide RNA (sgRNA) delivery using PCR-generated DNA templates which are transcribed in vivo by T7 RNA polymerase and an online resource (LeishGEdit...
May 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28564555/holocarboxylase-synthetase-a-moonlighting-transcriptional-coregulator-of-gene-expression-and-a-cytosolic-regulator-of-biotin-utilization
#12
REVIEW
Alfonso León-Del-Río, Viviana Valadez-Graham, Roy A Gravel
The vitamin biotin is an essential nutrient for the metabolism and survival of all organisms owing to its function as a cofactor of enzymes collectively known as biotin-dependent carboxylases. These enzymes use covalently attached biotin as a vector to transfer a carboxyl group between donor and acceptor molecules during carboxylation reactions. In human cells, biotin-dependent carboxylases catalyze key reactions in gluconeogenesis, fatty acid synthesis, and amino acid catabolism. Biotin is attached to apocarboxylases by a biotin ligase: holocarboxylase synthetase (HCS) in mammalian cells and BirA in microbes...
August 21, 2017: Annual Review of Nutrition
https://www.readbyqxmd.com/read/28553299/screening-of-proximal-and-interacting-proteins-in-rice-protoplasts-by-proximity-dependent-biotinylation
#13
Qiupeng Lin, Zejiao Zhou, Wanbin Luo, Maichun Fang, Meiru Li, Hongqing Li
Proximity-dependent biotin identification (BioID), which detects physiologically relevant proteins based on the proximity-dependent biotinylation process, has been successfully used in different organisms. In this report, we established the BioID system in rice protoplasts. Biotin ligase BirAG was obtained by removing a cryptic intron site in the BirA(∗) gene when expressed in rice protoplasts. We found that protein biotinylation in rice protoplasts increased with increased expression levels of BirAG. The biotinylation effects can also be achieved by exogenous supplementation of high concentrations of biotin and long incubation time with protoplasts...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28475612/calmodulin-like-proteins-localized-to-the-conoid-regulate-motility-and-cell-invasion-by-toxoplasma-gondii
#14
Shaojun Long, Kevin M Brown, Lisa L Drewry, Bryan Anthony, Isabelle Q H Phan, L David Sibley
Toxoplasma gondii contains an expanded number of calmodulin (CaM)-like proteins whose functions are poorly understood. Using a combination of CRISPR/Cas9-mediated gene editing and a plant-like auxin-induced degron (AID) system, we examined the roles of three apically localized CaMs. CaM1 and CaM2 were individually dispensable, but loss of both resulted in a synthetic lethal phenotype. CaM3 was refractory to deletion, suggesting it is essential. Consistent with this prediction auxin-induced degradation of CaM3 blocked growth...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28470616/in-vivo-biotinylation-of-antigens-in-e-coli
#15
Susanne Gräslund, Pavel Savitsky, Susanne Müller-Knapp
Site-specific biotinylation of proteins is often the method of choice to enable efficient immobilization of a protein on a surface without interfering with protein folding. The tight interaction of biotin and streptavidin is frequently used to immobilize an antigen during phage display selections of binders. Here we describe a method of in vivo biotinylation of proteins during expression in E. coli, by tagging the protein with the short biotin acceptor peptide sequence, Avi tag, and co-expression of the E. coli biotin ligase (BirA) resulting in precise biotinylation of a specific lysine residue in the tag...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28466579/a-conserved-regulatory-mechanism-in-bifunctional-biotin-protein-ligases
#16
Jingheng Wang, Dorothy Beckett
Class II bifunctional biotin protein ligases (BirA), which catalyze post-translational biotinylation and repress transcription initiation, are broadly distributed in eubacteria and archaea. However, it is unclear if these proteins all share the same molecular mechanism of transcription regulation. In Escherichia coli the corepressor biotinoyl-5'-AMP (bio-5'-AMP), which is also the intermediate in biotin transfer, promotes operator binding and resulting transcription repression by enhancing BirA dimerization...
August 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28463988/translocation-of-the-papillomavirus-l2-vdna-complex-across-the-limiting-membrane-requires-the-onset-of-mitosis
#17
Christine M Calton, Matthew P Bronnimann, Ariana R Manson, Shuaizhi Li, Janice A Chapman, Marcela Suarez-Berumen, Tatum R Williamson, Sudheer K Molugu, Ricardo A Bernal, Samuel K Campos
The human papillomavirus type 16 (HPV16) L2 protein acts as a chaperone to ensure that the viral genome (vDNA) traffics from endosomes to the trans-Golgi network (TGN) and eventually the nucleus, where HPV replication occurs. En route to the nucleus, the L2/vDNA complex must translocate across limiting intracellular membranes. The details of this critical process remain poorly characterized. We have developed a system based on subcellular compartmentalization of the enzyme BirA and its cognate substrate to detect membrane translocation of L2-BirA from incoming virions...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28454708/functional-characterisation-of-burkholderia-pseudomallei-biotin-protein-ligase-a-toolkit-for-anti-melioidosis-drug-development
#18
Thomas E H Bond, Alanna E Sorenson, Patrick M Schaeffer
Burkholderia pseudomallei (Bp) is the causative agent of melioidosis. The bacterium is responsible for 20% of community-acquired sepsis cases and 40% of sepsis-related mortalities in northeast Thailand, and is intrinsically resistant to aminoglycosides, macrolides, rifamycins, cephalosporins, and nonureidopenicillins. There is no vaccine and its diagnosis is problematic. Biotin protein ligase (BirA) which is essential for fatty acid synthesis has been proposed as a drug target in bacteria. Very few bacterial BirA have been characterized, and a better understanding of these enzymes is necessary to further assess their value as drug targets...
June 2017: Microbiological Research
https://www.readbyqxmd.com/read/28381627/characterization-of-rbp9-and-rbp10-two-developmentally-regulated-rna-binding-proteins-in-trypanosoma-brucei
#19
Luis Miguel De Pablos, Steve Kelly, Janaina de Freitas Nascimento, Jack Sunter, Mark Carrington
The fate of an mRNA is determined by its interaction with proteins and small RNAs within dynamic complexes called ribonucleoprotein complexes (mRNPs). In Trypanosoma brucei and related kinetoplastids, responses to internal and external signals are mainly mediated by post-transcriptional processes. Here, we used proximity-dependent biotin identification (BioID) combined with RNA-seq to investigate the changes resulting from ectopic expression of RBP10 and RBP9, two developmentally regulated RNA-binding proteins (RBPs)...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28336960/co-expression-of-bira-with-biotin-bait-achieves-in-vivo-biotinylation-of-overexpressed-stable-n-glycosylated-srage-in-transgenic-silkworms
#20
Miyuki Kumano-Kuramochi, Ken-Ichiro Tatematsu, Mayumi Ohnishi-Kameyama, Mari Maeda-Yamamoto, Toshiro Kobori, Hideki Sezutsu, Sachiko Machida
Here, we demonstrated the expression of the N-glycosylated extracellular ligand binding domain of receptor for advanced glycation end products (sRAGE) in middle silk glands (MSGs) of transgenic silkworms using the GAL4/UAS system. Over 1 mg of sRAGE was obtained from one transgenic silkworm. sRAGE purified from the silkworm exhibited good stability and maintained specific ligand-binding ability. In addition, N-glycan analysis of sRAGE revealed that N-glucan completely lacked potentially allergenic fucose...
March 23, 2017: Scientific Reports
keyword
keyword
48093
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"